ArticlePloS one2017
De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae).
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
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- Development of Simple Sequence Repeat ofBiology · 2024Article
- De novo transcriptome assembly, annotation and SSR mining data of Hellula undalis (Fabr.) (Lepidoptera: Pyralidae), the cabbage webworm.Journal, genetic engineering & biotechnology · 2024Article
- De Novo Mining and Validating Novel Microsatellite Markers to Assess Genetic Diversity inGenes · 2023Article
- Article
- Article
- The phylogenetic and evolutionary analyses of detoxification gene families in Aphidinae species.PloS one · 2022Article
- Selection and Validation of Reference Genes For qRT-PCR Analysis ofFrontiers in physiology · 2021Article
- Genomic approach for conservation and the sustainable management of endangered species of the Amazon.PloS one · 2021Article
- Development and characterization of 16 novel microsatellite markers by Transcriptome sequencing for Angelica dahurica and test for cross-species amplification.BMC plant biology · 2020Article
- Genetic Variation May Have Promoted the Successful Colonization of the Invasive Gall Midge,Frontiers in genetics · 2020Article
- Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants.Molecules (Basel, Switzerland) · 2018Review
- Functional Analysis of a Carboxylesterase Gene Associated With Isoprocarb and Cyhalothrin Resistance inFrontiers in physiology · 2018Article
- Identification, Expression, and Regulation of an Omega Class Glutathione S-transferase inFrontiers in physiology · 2018Article
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Authors and funding
6 authors.
Funding
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Abstract
The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform. A total of 114.4 million raw reads with a GC content of 40.03% was generated. The raw reads were cleaned and assembled into 29,467 unigenes with an N50 length of 1,580 bp. Using several public databases, 82.47% of these unigenes were annotated. Of the annotated unigenes, 8,022 were assigned to COG pathways, 9,895 were assigned to GO pathways, and 14,586 were mapped to 257 KEGG pathways. A total of 7,936 potential microsatellites were identified in 5,564 unigenes, 60 of which were selected randomly and amplified using specific primer pairs. Fourteen loci were found to be polymorphic in the four R. padi populations. The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species.
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